Taxonomic assignment report

Department of Agriculture, Fisheries and Forestry logo
Facility Hogwarts
Analyst John Doe
Analysis started 2025-04-03 05:21:46
Analysis completed 2025-04-03 05:21:46
Wall time 0:0:0 hours

Sample details

locus 16S mitochondrial rRNA gene
preliminary_id Trogoderma
taxa_of_interest Trogoderma granarium
country Pakistan
host Rice
sample_id VE25-1428_16S
Query DNA sequence

Result overview

Trogoderma granarium
Positive species identification.
Reasoning - Flag 1A: 1 candidate species matched with high stringency (identity ≥ 98.5%).

Preliminary morphology ID confirmed True

Flag 7A: Candidate species is consistent with preliminary morphology ID

Taxa of interest ruled out False

Flag 2B: Taxon of interest detected

Flag 5.1C: The given locus for this taxon is not present in reference database (0 entries)

Flag 5.2C: ≤10% of taxon have reference sequence(s) at the given locus

Analyst evaluation

Identification of candidate species

Flag 1A: Positive species identification - Trogoderma granarium
1 candidate species matched with high stringency (identity ≥ 98.5%)

Candidate hits must meet ONE of these criteria:

Minimum alignment length 400bp
Minimum query coverage 85.0%

Candidate hits are then classified as follows:

Classification Alignment identity Number of hits Number of species
STRONG MATCH ≥ 98.5% 14 1
MODERATE MATCH ≥ 93.5% NA NA
NO MATCH < 93.5%

Hits per candidate species (top 10 candidates only)

Species Hits Identity E-value
Trogoderma granarium 14 100.0% 0.0

Analyst evaluation

Taxa of interest

This sections shows the taxa of interest specified by the submitter. Each of these taxa has been cross-referenced against the candidate species to determine if they might match the taxonomic identity of the sample. A blank row indicates a TOI that did not match any candidate species, meaning that it is unlikely that the sample matches that TOI.

Taxon of interest Match rank Match taxon Match species Match accession Match identity
Trogoderma granarium species Trogoderma granarium Trogoderma granarium MZ571637 1.0

See the Database coverage section to see database coverage for taxa of interest.

Reference sequence source diversity

This analysis evaluates how many independent sources have contributed to reference sequences for each candidate species. This provides a measure of confidence in the taxonomic annotation of references sequences. A sequence that has been annotated by multiple independent sources is more likely to have a correct taxonomic annotation.

Analyst evaluation

Independent sources

Flag 4A: Reference sequences are from diverse sources and therefore likely to be reliable
Reasoning: Matching sequence records for this species are from >5 independent sources (found 6 sources)

6 Independent Sources

The matching reference sequences for this species have been annotated by 6 independent source(s). A source is considered independent if the author list or publication title is distinct.

Source 1

Hit accession Automated Authors Title Journal
MZ571637 False Rako,L.
Agarwal,A.
Semeraro,L.
Broadley,A.
Rodoni,B.C.
Blacket,M.J.
A LAMP (loop-mediated isothermal amplification) test for rapid identification of Khapra beetle (Trogoderma granarium) Pest Manag Sci (2021) In press
MZ571637 False Blacket,M.
Rako,L.
Agarwal,A.
Direct Submission Submitted (13-JUL-2021) AVR, Agriculture Victoria, AgriBio, Bundoora, Victoria 3083, Australia
MZ571636 False Rako,L.
Agarwal,A.
Semeraro,L.
Broadley,A.
Rodoni,B.C.
Blacket,M.J.
A LAMP (loop-mediated isothermal amplification) test for rapid identification of Khapra beetle (Trogoderma granarium) Pest Manag Sci (2021) In press
MZ571636 False Blacket,M.
Rako,L.
Agarwal,A.
Direct Submission Submitted (13-JUL-2021) AVR, Agriculture Victoria, AgriBio, Bundoora, Victoria 3083, Australia

Source 2

Hit accession Automated Authors Title Journal
KJ930431 False Olson,R.L.O.
Farris,R.E.
Barr,N.B.
Cognato,A.I.
Molecular identification of Trogoderma granarium (Coleoptera: Dermestidae) using the 16S gene Unpublished
KJ930431 False Olson,R.L.O.
Farris,R.E.
Barr,N.B.
Cognato,A.I.
Direct Submission Submitted (02-JUN-2014) Center for Learning Innovation, University of Minnesota, Rochester, 111 South Broadway Suite 300, Rochester, MN 55904, USA
KJ930432 False Olson,R.L.O.
Farris,R.E.
Barr,N.B.
Cognato,A.I.
Molecular identification of Trogoderma granarium (Coleoptera: Dermestidae) using the 16S gene Unpublished
KJ930432 False Olson,R.L.O.
Farris,R.E.
Barr,N.B.
Cognato,A.I.
Direct Submission Submitted (02-JUN-2014) Center for Learning Innovation, University of Minnesota, Rochester, 111 South Broadway Suite 300, Rochester, MN 55904, USA
KJ930452 False Olson,R.L.O.
Farris,R.E.
Barr,N.B.
Cognato,A.I.
Molecular identification of Trogoderma granarium (Coleoptera: Dermestidae) using the 16S gene Unpublished
KJ930452 False Olson,R.L.O.
Farris,R.E.
Barr,N.B.
Cognato,A.I.
Direct Submission Submitted (02-JUN-2014) Center for Learning Innovation, University of Minnesota, Rochester, 111 South Broadway Suite 300, Rochester, MN 55904, USA
KJ930433 False Olson,R.L.O.
Farris,R.E.
Barr,N.B.
Cognato,A.I.
Molecular identification of Trogoderma granarium (Coleoptera: Dermestidae) using the 16S gene Unpublished
KJ930433 False Olson,R.L.O.
Farris,R.E.
Barr,N.B.
Cognato,A.I.
Direct Submission Submitted (02-JUN-2014) Center for Learning Innovation, University of Minnesota, Rochester, 111 South Broadway Suite 300, Rochester, MN 55904, USA

Source 3

Hit accession Automated Authors Title Journal
OM388538 False mzhr,N.N.
Jawad,M.M.
Sabr,A.J.
Direct Submission Submitted (25-JAN-2022) biology, Baghdad university, palestine street, baghdad, baghgdad 10046, Iraq
OM389182 False mzhr,N.N.
Jawad,M.M.
Sabr,A.J.
Direct Submission Submitted (25-JAN-2022) biology, Baghdad university, palestine street, baghdad, baghgdad 10046, Iraq
OM388512 False Mzhr,N.N.
Jawad,M.M.
Sabr,A.J.
Direct Submission Submitted (25-JAN-2022) biology, Baghdad university, palestine street, baghdad, baghgdad 10046, Iraq
OM388567 False Mzhr,N.N.
Jawad,M.M.
Sabr,A.J.
Direct Submission Submitted (25-JAN-2022) biology, Baghdad university, palestine street, baghdad, baghgdad 10046, Iraq
OM389131 False Mzhr,N.N.
Jawad,M.M.
Sabr,A.J.
Direct Submission Submitted (25-JAN-2022) biology, Baghdad university, palestine street, baghdad, baghgdad 10046, Iraq

Source 4

Hit accession Automated Authors Title Journal
LC386208 False Furui,S.
Miyanoshita,A.
Imamura,T.
Minegishi,Y.
Kokutani,R.
Qualitative real-time PCR identification of the khapra beetle, Trogoderma granarium (Coleoptera: Dermestidae) Appl. Entomol. Zool. (Jpn.) 54, 101-107 (2019)
LC386208 False Furui,S.
Minegishi,Y.
Kokutani,R.
Direct Submission Submitted (28-MAY-2018) Contact:Satoshi Furui Food Research Institute, NARO, Food Entomology Laboratory; 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan URL :http://www.naro.affrc.go.jp/english/index.html

Source 5

Hit accession Automated Authors Title Journal
ON725093 False Kavallieratos,N.G.
Boukouvala,M.C.
Lorentha Gidari,D.
Di Giuseppe,G.
Canale,A.
Benelli,G.
Does cross-mating affect behavioral asymmetries and mating success of Trogoderma granarium strains? Unpublished
ON725093 False Di Giuseppe,G. Direct Submission Submitted (10-JUN-2022) Department of Biology, University of Pisa, Italy, Via A. Volta, 4, Pisa, PI I-56126, Italy

Source 6

Hit accession Automated Authors Title Journal
NC_053875 False Zeng,L.
Pang,Y.
Feng,S.
Wang,Y.
Stejskal,V.
Aulicky,R.
Zhang,S.
Li,Z.
Comparative mitochondrial genomics of five Dermestid beetles (Coleoptera: Dermestidae) and its implications for phylogeny Genomics (2020) In press
NC_053875 False Direct Submission Submitted (25-MAR-2021) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
NC_053875 False Zeng,L.
Pang,Y.
Li,Z.
Direct Submission Submitted (25-FEB-2020) Department of Entomology, College of Plant Protection, China Agricultural University, Yuanmingyuan West Road 2#, Haidian District, Beijing 100193, China

Database coverage of target taxa

The target taxa include candidate species, the preliminary morphology ID, and any taxa of interest provided by the submitter. Each of these taxa are independently evaluated against the reference database to determine whether sufficient reference data exists to support identification of the target taxon. Insufficient coverage of a taxon can result in that taxon not be correctly identified as the taxonomic identity of the sample. For example, if the sample is Homo sapiens, but Homo sapiens sequences are not included in the reference database, the analysis will be unable to identity Homo sapiens as the correct taxonomic identity, and will most likely assign the closest relative with reference data as the taxonomic identity.

Analyst evaluation

Database coverage

Flag 5.1C: The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)


Database coverage of Trogoderma granarium

Flag 5.1C: The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)

0 records

There are 0 sequences in the reference database for Trogoderma granarium at the given locus 16S mitochondrial rRNA gene.

Map of database coverage

Database coverage of species in genus Trogoderma

Flag 5.2C: The database has poor support for species in this genus
Reasoning: ≤10% of taxon have reference sequence(s) at the given locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Trogoderma
  • At the target locus 16S mitochondrial rRNA gene

Number of GenBank records at locus 16S mitochondrial rRNA gene


Database coverage of species in genus Trogoderma that occur in country of origin

Flag 5.3C: Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: No species in genus have been observed in the country of origin

/ (%) sequence records were found in the reference database for:

  • Species in the genus Trogoderma
  • At the target locus 16S mitochondrial rRNA gene
  • In the sample country of origin Pakistan

Number of GenBank records at locus 16S mitochondrial rRNA gene

Database coverage

Flag 5.1C: The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)


Database coverage of Trogoderma

Flag 5.1C: The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)

0 records

There are 0 sequences in the reference database for Trogoderma at the given locus 16S mitochondrial rRNA gene.

Map of database coverage

Database coverage of species in genus Trogoderma

Flag 5.2C: The database has poor support for species in this genus
Reasoning: ≤10% of taxon have reference sequence(s) at the given locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Trogoderma
  • At the target locus 16S mitochondrial rRNA gene

Number of GenBank records at locus 16S mitochondrial rRNA gene


Database coverage of species in genus Trogoderma that occur in country of origin

Flag 5.3A: Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: All species in genus from country of origin have reference sequence(s) for this locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Trogoderma
  • At the target locus 16S mitochondrial rRNA gene
  • In the sample country of origin Pakistan

Number of GenBank records at locus 16S mitochondrial rRNA gene

Database coverage

Flag 5.1C: The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)


Database coverage of Trogoderma granarium

Flag 5.1C: The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)

0 records

There are 0 sequences in the reference database for Trogoderma granarium at the given locus 16S mitochondrial rRNA gene.

Map of database coverage

Database coverage of species in genus Trogoderma

Flag 5.2C: The database has poor support for species in this genus
Reasoning: ≤10% of taxon have reference sequence(s) at the given locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Trogoderma
  • At the target locus 16S mitochondrial rRNA gene

Number of GenBank records at locus 16S mitochondrial rRNA gene


Database coverage of species in genus Trogoderma that occur in country of origin

Flag 5.3C: Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: No species in genus have been observed in the country of origin

/ (%) sequence records were found in the reference database for:

  • Species in the genus Trogoderma
  • At the target locus 16S mitochondrial rRNA gene
  • In the sample country of origin Pakistan

Number of GenBank records at locus 16S mitochondrial rRNA gene

Intraspecies diversity

This section provides a phylogeny of the candidate reference sequences. The analyst can use this to make a subjective observation on how well the reference sequences are able to distinguish between species. If the phylogeny shows distinct clades for each species, we can be confident that the molecular data are capable of distinguishing between those species. However, if the phylogeny shows overlap between species, this reduces the capacity of the molecular data to confidently distinguish between those species. In some cases, we may see the query sequence falling outside of the adjacent species' clades, which indicates that our query species is not represented in the reference database, which could indicate a rare or novel species.

Analyst evaluation

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The phylogetic tree was constructed with FastME using the Neighbor-Joining method. Multiple-sequence alignment of the candidate reference sequences was performed using MAFFT. The visualization is rendered with TidyTree.

Taxonomy Check

The following resources can be used to ensure that the given taxonomy is legitimate and current.

Taxa Database
General GBIF
General ITIS
Mealybugs & scale ScaleNet database
Thrips Thripswiki
Spider Mites Spider Mites Database
Psocodea (Barklice, Booklice, and Parasitic Lice) Psocodea Species File Online
Orthoptera Orthoptera Species File Online
Drosophilidae TaxoDros
Diptera Catalog of the Diptera of the Australasian and Oceanian Regions
Systema Dipterorum
Aphids Aphid Species File
Ants AntWeb
AntCat
Lepidoptera (butterflies and moths) The Global Lepidoptera Names Index
Gracillariidae (primitive moths) Global Taxonomic Database of Gracillariidae
Pyralidae (pyralid moths) Global Information System on Pyraloidea
Tortricidae (tortrix moths) Tortricidae Resources on the Net